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Taxon Constraint for His-Purkinje system in fish #12451
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You want to add these constraints, correct? |
?Yes Tanya, Thank you Michael E. Rice AgBase biocurator From: Tanya Berardini notifications@github.com You want to add these constraints, correct? You are receiving this because you authored the thread. |
Your list:
What about GO:0003164, His-Purkinje system development ? There are 34 terms that contain the word 'Purkinje', 20 that contain 'bundle of His'. Do you mean to add the taxon restrictions to all of these (some will inherit the restriction by parentage) or just the specific subset that you put in your original request? |
Tanya, all of the terms containing His and Purkinje should be covered by the restriction. sorry, when I saw how many there are I did not finish the list thinking it would be covered by the review process. Thanks for working on this. Mike Michael E. Rice AgBase biocurator From: Tanya Berardini notifications@github.com Your list:
What about GO:0003164, His-Purkinje system development ? There are 34 terms that contain the word 'Purkinje', 20 that contain 'bundle of His'. Do you mean to add the taxon restrictions to all of these (some will inherit the restriction by parentage) or just the specific subset that you put in your original request? You are receiving this because you authored the thread. |
Hi Mike - With the giant number of open Github tickets and the relatively small amount of ontology editors' time, the best chance for getting things done quickly is to provide as much detail in the request as possible. :) Thanks for the clarification. |
? ok, thanks sorry for the incompleteness. Michael E. Rice AgBase biocurator From: Tanya Berardini notifications@github.com Hi Mike - With the giant number of open Github tickets and the relatively small amount of ontology editors' time, the best chance for getting things done quickly is to provide as much detail in the request as possible. :) Thanks for the clarification. You are receiving this because you authored the thread. |
Looked into this issue a little further:
@michaelerice: Can you figure out which terms in UBERON are the most appropriate to restrict to the taxa that you requested? Here's a search I did for His-Purkinje using AmiGO I was thinking this one: http://amigo.geneontology.org/amigo/term/UBERON:0004146 @cmungall - you might be interested in this ticket blocked on #12223 |
I am very interested We have grouped the teleost (and thus Actinopterygii) distal conduction system in with His-Purkinje system The evidence may have been weak. E.g. ZFA uses "His-Purkinji network" as an exact syn. This was an early merge in uberon What is the relationship between these structures? Haven't had time to read the references. Summoning homology and comparative fish anatomy people: @ANiknejad @mellybelly @ybradford @cerivs |
Ah OK, so the original ZFA entry was a mistake, it has been obsoleted:
From a skim of the refs it seems that lower vertebrates have a functional analog but is histologically different; the functional analog is the trabecular layer |
OK, I think the representation of the analogous tissue in uberon has a lot of gaps I'd like to fill, but we should take that over to the uberon tracker For now I will add the required TC, and we'll call this ticket closed btw, I am going be bold and rewrite the TC as only-in tetrapoda (the 3 negative constraints as originally stated leaves open the possibility of the HPS being in Chondrichthyes, or even in cyclostomes, but this seems biologically unlikely based on the 3 papers here) |
Request review for taxon constraint for HIs-Purkinje GO terms
GO:0060933
GO:0060934
GO:0060933
GO:0003168
GO:0086054
GO:0086055
GO:0086028
GO:0086073
GO:0086078
never_in_taxon Actinopterygii 7898, Coelacanthiformes 7894, Dipnoi 7878
PMID: 12626327 PMID: 21234997
Thank you
GOC:MR
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